In a trio of studies published on June 27 in the journal Nature Microbiology, researchers at The University of Texas at Austin have discovered “fingerprints” of mysterious viruses hidden in an ancient group of microbes that may include the ancestors of all complex life on Earth: from fungi to plants to humans.
Ths discovery is significant; it explores the hypothesis that viruses were imperative to the evolution of humans and other complex life forms.
These microbes – known as Asgard archaea after the abode of the gods in Norse mythology – are usually found in the frigid sediments deep in the ocean and in boiling springs, and existed on Earth before the first eukaryotic cells, which carry their DNA inside a nucleus.
Some scientists have hypothesized that viruses may have played in role in how life forms first came to be by infecting the Asgard archaea. They may have even given rise to some of the first precursors to the nucleus. But, no Asgard-infecting viruses had been discovered hitherto. The latest research by Ian Rambo (a former doctoral student at UT Austin) and other members of Brett Baker’s lab sheds light on how viruses might have played a role in this billions-year-old history.
“These are the first studies investigating Asgard archaeal viruses; there was nothing known before,” Susanne Erdmann, group leader of the archaeal virology research group at the Max Planck Institute for Marine Microbiology in Bremen, Germany, who was not involved in the studies, told Live Science. In the future, this line of research may reveal if and how viruses were involved in the emergence of eukaryotic cells on Earth, she said.
‘An adaptive immune system’
In the new research, scientists searched for evidence of viral infection embedded in the DNA of Asgard archaea – which comes in the form of viral DNA called “CRISPR spacers.”
According to Rambo, most people who think of CRISPR relate it to the famous gene-editing tool that allows scientists to easily manipulate genetic sequences. This tool was originally adapted from the natural defense mechanisms of bacteria and archaea.
CRISPR refers to a region of DNA made up of short, repeated sequences with “spacers” sandwiched between each repeat. Interestingly, bacteria and archaea swipe these spacers from viruses that infect them, and the cells maintain a memory bank of viral DNA that helps them recognize the viruses should they attack again.
“It’s an adaptive immune system that remembers these previous infections,” said Rambo, who is now a postdoctoral scholar with the USDA’s Agricultural Research Service.
Rambo and his colleagues had hunted in the Guaymas Basin in the Gulf of California – the body of water between Baja California and mainland Mexico – for such DNA spacers in Asgard archaea specimens collected from sediments near hydrothermal vents, roughly 1.25 miles (2 kilometers) beneath the water’s surface.
The team matched the spacers they found to longer stretches of viral DNA gathered from the deep-sea environment.
Many more Asgard-infecting viruses are yet to be discovered
The researchers could infer the kinds of proteins the various genes code for and how the viruses might function, working with viral DNA.
But, eventually, they could only figure out the functions of some of the viruses’ genes; the functions of the vast majority of the genes are still unknown, Erdmann said. Also, because CRISPR doesn’t work against all viruses, many more Asgard-infecting viruses are yet to be discovered, she said.
These hidden viruses could be found by growing Asgard archaea in the lab. “However, culturing Asgard archaea has been proven very difficult,” Erdmann said. Until now, only one research group has managed to culture Asgard archaea, and it took them 12 long years to do it as archaeal cells take weeks to replicate.
But until more Asgards can be grown in the lab, CRISPR spacer matching is probably the most efficient way to find more viruses, Krupovic said. As more viruses are found, their role in the emergence of eukaryotes, including humans, may gain more clarity, added Rambo.